Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana

Microsatellite resources of Eucalyptus: current status and future perspectives

Eucalyptus is the premier paper pulp, short rotation plantation species grown all over the world. Genetic improvement programs integrating molecular marker tools are in progress in many parts of the globe to increase the productivity. Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. Further, highly informative SSRs were used for the clonal identity, genetic fidelity and in certification of breeder's rights. Eucalyptus genetic linkage maps generated with microsatellite loci were used successfully to identify quantitative trait loci (QTLs) for various economically important traits. Progressively more numbers of microsatellites are being linked to genes associated with adaptive and functional variations, therefore making their utility broader in genetic applications. Availability of common SSR markers across the species provides an opportunity to validate the expression of QTLs across variable genetic backgrounds and accurately compare the position of QTLs in other species. Recent evidences suggest that the presence of SSRs in micro RNAs of plant species play a role in the quantitative trait expression. Similar studies in eucalypts may provide new insights into the genetic architecture of transcript-level variations and post transcriptional gene regulation. This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection.

Effects of harvesting of increasing intensities on genetic diversity and population structure of white spruce

Forest harvesting of increasing intensities is expected to have intensifying impacts on the genetic diversity and population structure of postharvest naturally regenerated stands by affecting the magnitude of evolutionary processes, such as genetic drift, gene flow, mating system, and selection. We have tested this hypothesis for the first time by employing widely distributed boreal white spruce (Picea glauca) as a model and controlled, replicated experimental harvesting and regeneration experiment at the EMEND project site (http://www.emendproject.org). We used two approaches. First, genetic diversity and population structure of postharvest natural regeneration after five harvesting treatments (green tree retention of 75%, 50%, 20%, and 10%, and clearcut) were assessed and compared with those of the unharvested control (pristine preharvest old-growth) in two replicates each of conifer-dominated (CD) and mixed-wood (MW) forest, using 10 (six EST (expressed sequence tag) and four genomic) microsatellite markers. Second, genetic diversity and population structure of preharvest old-growth were compared with those of postharvest natural regeneration after five harvesting treatments in the same treatment blocks in one replicate each of CD and MW forests. Contrary to our expectations, genetic diversity, inbreeding levels, and population genetic structure were similar between unharvested control or preharvest old-growth and postharvest natural regeneration after five harvesting treatments, with clearcut showing no negative genetic impacts. The potential effects of genetic drift and inbreeding resulting from harvesting bottlenecks were counterbalanced by predominantly outcrossing mating system and high gene flow from the residual and/or surrounding white spruce. CD and MW forests responded similarly to harvesting of increasing intensities. Simulated data for 10, 50, and 100 microsatellite markers showed the same results as obtained empirically from 10 microsatellite markers. Similar patterns of genetic diversity and population structure were observed for EST and genomic microsatellites. In conclusion, harvesting of increasing intensities did not show any significant negative impact on genetic diversity, population structure, and evolutionary potential of white spruce in CD and MW forests. Our first of its kind of study addresses the broad central forest management question how forest harvesting and regeneration practices can best maintain genetic biodiversity and ecosystem integrity.

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.

Application of plant DNA markers in forensic botany: Genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites

As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

Genetic Structure Inside a Declining Red Oak Community in Old-Growth Forest

Problems with oak regeneration have been documented in the last 50 years at numerous sites in the Midwestern United States. We applied nuclear microsatellites to examine the demographic and fine-scale spatial genetic structure of red oaks in two old-growth stands in Indiana. Oaks in one stand have declined in numbers over the past several decades whereas oaks in the other, smaller stand have increased. Large amounts of genetic variation were maintained within stands, and there was slight but significant differentiation among stands. There was significant but weak isolation by distance genetic structure within the large stand, likely reflecting family structure. No significant differences exist in allele frequencies or in levels of genetic diversity between cohorts that remain well represented within each stand, even between medium-sized adults and those antedating European settlement of the area. However, a virtual absence of smaller size classes in the forest interior of the large stand represents the early stages of a genetic bottleneck in what had been the core habitat of this stand. Whether future generations of this old-growth stand will retain the present genetic character depends on the oaks regenerating at the forest margins, absent any major changes in disturbance regimes. Similar demographic and genetic dynamics are likely occurring in a large number of remnant oak forests across the Midwest.